"Tools or methods to convert PDF to Markdown" matching MCP servers:

Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.

Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

Enables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Natural language-driven spatial transcriptomics analysis via MCP. Integrates 60+ methods for preprocessing, visualization, spatial statistics, cell communication, deconvolution, and trajectory analysis.

An MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.

Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.

MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.

A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.

Enables agents to search a public PubMed-derived corpus by natural language or identifiers and to retrieve publication details while traversing bounded citation and semantic literature graphs.

Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.

Provides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.

Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.

A high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, and structural biology.

A bioinformatics MCP server that connects AI clients to over 30 life science databases and 32 curated tools for research, drug discovery, and clinical analysis.

Leverages large language models to analyze users' WeGene genetic testing reports, providing access to report data via custom URI schemes and enabling profile and report management through OAuth authentication and API utilization.